Hi James,

> So now we look at the main effect of Context and we see a cluster in the angular gyrus. The question remains,
> what is causing the significant F. All three conditions could differ from one another or it could be one condition
> driving the effect. I would (really!) like to provide a valid answer to that question, but I still don't see how without
> doing some averaging over the voxels in the cluster identified by the omnibus F.

It seems to me that you can run exactly the same tests as whatever you're doing at the cluster level through averaging across the voxels. And they are basically three pairwise comparisons, right?

> My plan was to compare the differences between conditions in the cluster via averaging but I am getting the
> impression that I can't do this?

Well, I don't have a strong opinion about this circularity issue. Instead it is the reviewers that you would have to try to convince with your approach.

> Specifically, the hypothesis we actually had was that HC > LC, and the comparison of LC vs NC is really
> meant as a type of sanity check. I get that defining a cluster by HC > LC at the whole-brain level biases
> the LC vs NC test but I feel as though the cluster from the ANOVA is not inherently biased in the same
> way since really any difference between means could have caused it.

Averaging does change the cross-subject variability especially when the precision/reliability information due to the averaging step is typically not taken into consideration. How about this: you run both voxel-wise and cluster-level analyses, and, if the two results are consistent, the cluster-level analysis would be more convincing.

> I am not trying to make a strong assertion about the null. It's just that it seems to me there are two
> interesting possibilities (among other ones) and I would like to tell them apart. One is that a region
> responds to both types of context in a linear fashion (and since HC as more context than LC you
> get an increase such that NC < LC < HC), and the other is that it responds specifically to the
> information in the HC condition.

In addition to the *statistical* inference regarding the linearity, I would reinforce the conclusion with the *physical* evidence of the BOLD response magnitude of the three conditions, for example, with graphs.

> This is where I get confused. To run this ANOVA I would have to average within the cluster. So why
> can I not average within the cluster to compare conditions after the whole-brain ANOVA above but
> can average to run this ANOVA? I feel as though I am missing something.

Yes, for this part, you do have to perform the averaging before you could run region-by-condition ANOVA.

Gang